Comprehensive proteomic and metabolomic profiling of mcr-1 mediated colistin resistance in Escherichia coli

Abstract

19The spread of mcr-1 in human and veterinary medicine has jeopardized the use of 20 polymyxins, the last-resort antibiotics against life-threatening multidrug-resistant 21 Gram-negative bacteria. As a lipid-modified gene, whether mcr-1 brings proteomic and 22 metabolomic changes in the bacteria and affects the corresponding metabolic pathway 23 is largely unknown. Herein, we used label-free quantitative proteomics and untargeted 24 metabolomics to profile comprehensive proteome and metabolome characteristics of 25 mcr-1-mediated colistin-resistant and -sensitive Escherichia coli and further insight the 26 resistant mechanism of colistin. We identified large sets of differential expression 27 proteins and metabolites that contributed to mcr-1-mediated antibiotic resistance 28 predominantly in the different growth conditions with and without colistin. mcr-1 could 29 cause the down-regulated expression of most proteins to adapt drug pressure. Pathway 30 analysis showed that metabolic process was significantly affected, mainly related to 31 glycerophospholipid metabolism, thiamine metabolism, and lipopolysaccharide 32 biosynthesis. The substrate phosphatidylethanolamine for mcr-1 to mediate colistin 33 resistance is accumulated in colistin-resistant E. coli. Notably, mcr-1 can not only cause 34 the phosphoethanolamine modification of bacterial cell membrane lipid A, but also 35 affect the biosynthesis and transport of lipoprotein in colistin resistance through 36 disturbing the expression of efflux pump proteins involved in cationic antibacterial 37 peptide resistance pathway. Overall, the disturbed glycerophospholipid metabolism, 38 lipopolysaccharide biosynthesis and the accumulation of the substrate 39 phosphatidylethanolamine is closely related with mcr-1-mediated colistin resistance 3 40and these findings can further provide valuable information to inhibit colistin resistance 41 by blocking this metabolic process. 43Since the discovery of the plasmid-mediated colistin resistance determinant mcr-1 46 in Enterobacteriace in 2015, its widespread dissemination brings potential threats to the 47 treatment of extensively drug resistant bacterial infections in animals and humans. 48Although many excellent achievements in its epidemic evidence and resistance 49 mechanism have been made, the in-depth colistin resistance mechanisms, such as the 50 omics profile of bacteria mediated by mcr-1 in Escherichia coli needs further research. 51 In this study, comprehensive proteomic and metabolomic profiles of mcr-1-mediated 52 colistin-resistant and -sensitive Escherichia coli were investigated to clarify the protein 53 and metabolite features related to mcr-1. The proteome characteristics of colistin-54 resistant E. coli carrying mcr-1 under different selection pressures of colistin and 55 polymyxin B were investigated, and the metabolic pathways including 56 glycerophospholipid metabolism, thiamine metabolism, and lipopolysaccharide 57 biosynthesis were disturbed. Up to 67 differential metabolites were identified in mcr...